Species assembly in model ecosystems, I: Analysis of the population model and the invasion dynamics

Recently we have introduced a simplified model of ecosystem assembly (Capitán et al., 2009) for which we are able to map out all assembly pathways generated by external invasions in an exact manner. In this paper we provide a deeper analysis of the model, obtaining analytical results and introducing some approximations which allow us to reconstruct the results of our previous work. In particular, we show that the population dynamics equations of a very general class of trophic-level structured food-web have an unique interior equilibrium point which is globally stable. We show analytically that communities found as end states of the assembly process are pyramidal and we find that the equilibrium abundance of any species at any trophic level is approximately inversely proportional to the number of species in that level. We also find that the per capita growth rate of a top predator invading a resident community is key to understand the appearance of complex end states reported in our previous work. The sign of these rates allows us to separate regions in the space of parameters where the end state is either a single community or a complex set containing more than one community. We have also built up analytical approximations to the time evolution of species abundances that allow us to determine, with high accuracy, the sequence of extinctions that an invasion may cause. Finally we apply this analysis to obtain the communities in the end states. To test the accuracy of the transition probability matrix generated by this analytical procedure for the end states, we have compared averages over those sets with those obtained from the graph derived by numerical integration of the Lotka-Volterra equations. The agreement is excellent.     

Biodiversity in model ecosystems, II: species assembly and food web structure

This is the second of two papers dedicated to the relationship between population models of competition and biodiversity. Here, we consider species assembly models where the population dynamics is kept far from fixed points through the continuous introduction of new species, and generalize to such models the coexistence condition derived for systems at the fixed point. The ecological overlap between species and shared preys, that we define here, provides a quantitative measure of the effective interspecies competition and of the trophic network topology. We obtain distributions of the overlap from simulations of a new model based both on immigration and speciation, and show that they are in good agreement with those measured for three large natural food webs. As discussed in the first paper, rapid environmental fluctuations, interacting with the condition for coexistence of competing species, limit the maximal biodiversity that a trophic level can host. This horizontal limitation to biodiversity is here combined with either dissipation of energy or growth of fluctuations, which in our model limit the length of food webs in the vertical direction. These ingredients yield an effective model of food webs that produce a biodiversity profile with a maximum at an intermediate trophic level, in agreement with field studies.     

Bayesian Inference for the Spatio-Temporal Invasion of Alien Species

In this paper we develop a Bayesian approach to parameter estimation in a stochastic spatio-temporal model of the spread of invasive species across a landscape. To date, statistical techniques, such as logistic and autologistic regression, have outstripped stochastic spatio-temporal models in their ability to handle large numbers of covariates. Here we seek to address this problem by making use of a range of covariates describing the bio-geographical features of the landscape. Relative to regression techniques, stochastic spatio-temporal models are more transparent in their representation of biological processes. They also explicitly model temporal change, and therefore do not require the assumption that the species' distribution (or other spatial pattern) has already reached equilibrium as is often the case with standard statistical approaches. In order to illustrate the use of such techniques we apply them to the analysis of data detailing the spread of an invasive plant, Heracleum mantegazzianum, across Britain in the 20th Century using geo-referenced covariate information describing local temperature, elevation and habitat type. The use of Markov chain Monte Carlo sampling within a Bayesian framework facilitates statistical assessments of differences in the suitability of different habitat classes for H. mantegazzianum, and enables predictions of future spread to account for parametric uncertainty and system variability. Our results show that ignoring such covariate information may lead to biased estimates of key processes and implausible predictions of future distributions.     

Biodiversity in model ecosystems, I: coexistence conditions for competing species

This is the first of two papers where we discuss the limits imposed by competition to the biodiversity of species communities. In this first paper, we study the coexistence of competing species at the fixed point of population dynamic equations. For many simple models, this imposes a limit on the width of the productivity distribution, which is more severe the more diverse the ecosystem is (1994, Theor. Popul. Biol. 45, 227-276). Here we review and generalize this analysis, beyond the "mean-field"-like approximation of the competition matrix used in previous works, and extend it to structured food webs. In all cases analysed, we obtain qualitatively similar relations between biodiversity and competition: the narrower the productivity distribution is, the more species can stably coexist. We discuss how this result, considered together with environmental fluctuations, limits the maximal biodiversity that a trophic level can host.     

Species matter: the role of competition in the assembly of congeneric bacteria

Interspecific competition is an important driver of community assembly in plants and animals, but phylogenetic evidence for interspecific competition in bacterial communities has been elusive. This could indicate that other processes such as habitat filtering or neutral processes are more important in bacterial community assembly. Alternatively, this could be a consequence of the lack of a consistent and meaningful species definition in bacteria. We hypothesize that competition in bacterial community assembly has gone undetected at least partly because overly broad measures of bacterial diversity units were used in previous studies. First, we tested our hypothesis in a simulation where we showed that how species are defined can dramatically affect whether phylogenetic overdispersion (a signal consistent with competitive exclusion) will be detected. Second, we demonstrated that using finer-scale Operational Taxonomic Units (OTUs) (with more stringent 16S rRNA sequence identity cutoffs or based on fast-evolving protein coding genes) in natural populations revealed previously undetected overdispersion. Finally, we argue that bacterial ecotypes, diversity units incorporating ecological and evolutionary theory, are superior to OTUs for the purpose of studying community assembly.     

The controlled assembly of microcosmic communities: the selective extinction hypothesis

Summary Forty communities were assembled through the controlled inoculation of algae, protozoans and a rotifer according to either of 2 distinct introduction schedules. These introduction schedules were constructed such that species reinvaded on average either every 6 or 8 w. Ten of the 20 beakers experiencing each invasion schedule contained 300 ml of media; the remaining beakers in each invasion category contained 100 ml of media. Species richness consistently increased throughout the initial 4 w and 7 w of the experiment for the low and high invasion rate beakers, respectively. The numbers of species in the low rate beakers were uncorrelated with time during the last half of the experiment; however, species richness gradually declined during this period in the high rate beakers. The extinction rate is shown to be disproportionately higher for large organisms in the small microcosms. Such selective extinction is consistent with the MacArthur-Wilson equilibrium model.     

Integrating internal and external dispersal in metacommunity assembly: preliminary theoretical analyses

Internal dispersal, which occurs among local communities within a metacommunity, and external dispersal, which supplies immigrants from outside the metacommunity, can both have a major impact on species diversity. However, few studies have considered the two simultaneously. Here I report preliminary computer-simulation results to suggest that internal and external dispersal can interact to influence species richness. Specifically, the results show that internal dispersal did not affect species richness under frequent external dispersal, whereas it enhanced richness in local communities while decreasing richness in metacommunities under infrequent external dispersal. Conversely, external dispersal influenced species richness in local communities more greatly in the absence of internal dispersal than in its presence, while external dispersal did not affect richness in metacommunities regardless of internal dispersal. Furthermore, internal and external dispersal interactively determined the importance of community assembly history in generating and maintaining variation in local community structure. Overall, these results suggest that the two dispersal types can reciprocally provide the context in which each affects species diversity and therefore that their effects cannot be understood in isolation of the other.Electronic Supplementary Material Supplementary material is available for this article at Tadashi Fukami is the recipient of the ninth Denzaburo Miyadi Award.     

线粒体电子传递系统的组装及其生物学意义

电子传递链亦称呼吸链,由位于线粒体内膜的I、II、III、IV 4种复合物组成,负责电子传递和产生质子梯度。电子主要从复合物I进入电子传递链,经复合物III传递至复合物IV。电子传递系统的组装是一个十分复杂的过程,目前已知主要有约69个结构亚基以及至少16个组装因子参与了人类复合物I、III、IV的组装,这些蛋白质由核基因组与线粒体基因组共同编码。对线粒体电子传递系统的蛋白质组成及其结构已研究得较为清楚,但对它们的组装了解得还比较初步。许多人类线粒体疾病是由于电子传递系统的功能障碍引起的,其中又有许多是由于该系统中一个或多个部件的错误组装引起的。研究这些缺陷不仅能够加深对线粒体疾病发病机理的了解,也有助于揭示线粒体功能的调控机制。将着重对电子传递系统复合物的组装及其与人类疾病关系的研究进展进行综述。     

Random walk in genome space: A key ingredient of intermittent dynamics of community assembly on evolutionary time scales

Community assembly is studied using individual-based multispecies models. The models have stochastic population dynamics with mutation, migration, and extinction of species. Mutants appear as a result of mutation of the resident species, while migrants have no correlation with the resident species. It is found that the dynamics of community assembly with mutations are quite different from the case with migrations. In contrast to mutation models, which show intermittent dynamics of quasi-steady states interrupted by sudden reorganizations of the community, migration models show smooth and gradual renewal of the community. As a consequence, instead of the 1/f diversity fluctuations found for the mutation models, 1/f², random-walk like fluctuations are observed for the migration models. In addition, a characteristic species-lifetime distribution is found: a power law that is cut off by a “skewed” distribution in the long-lifetime regime. The latter has a longer tail than a simple exponential function, which indicates an age-dependent species-mortality function. Since this characteristic profile has been observed, both in fossil data and in several other mathematical models, we conclude that it is a universal feature of macroevolution.     

Plant traits,species pools and the prediction of relative abundance in plant communities: a maximum entropy approach

Questions: To what extent can Shipley et al.'s original maximum entropy model of trait‐based community assembly predict relative abundances of species over a large (3000 km²) landscape? How does variation in the species pool affect predictive ability of the model? How might the effects of missing traits be detected? How can non‐trait‐based processes be incorporated into the model? Location: Central England. Material and Methods: Using 10 traits measured on 506 plant species from 1308 1‐m² plots collected over 3000 km² in central England, we tested one aspect of Shipley et al.'s original maximum entropy model of “pure” trait‐based community assembly (S₁), and modified it to represent both a neutral (S₂) and a hybrid (S₃) scenario of community assembly at the local level. Predictive ability of the three corresponding models was determined with different species pool sizes (30, 60, 100 and 506 species). Statistical significance was tested using a distribution‐free permutation test. Results: Predictive ability was high and significantly different from random expectations in S₁. Predictive ability was low but significant in S₂. Highest predictive ability occurred when both neutral and trait‐based processes were included in the model (S₃). Increasing the pool size decreased predictive ability, but less so in S₃. Incorporating habitat affinity (to indicate missing traits) increased predictive ability. Conclusions: The measured functional traits were significantly related to species relative abundance. Our results both confirm the generality of the original model but also highlight the importance of (i) taking into account neutral processes during assembly of a plant community, and (ii) properly defining the species pool.     

A two-stage model for the SIR outbreak: accounting for the discrete and stochastic nature of the epidemic at the initial contamination stage

The evolution of an infectious disease outbreak in an isolated population is split into two stages: a stochastic Markov process describing the initial contamination and a linked deterministic dynamical system with random initial conditions for the continued development of the outbreak. The initial contamination stage is well approximated by the randomized SI (susceptible/infected) model. We obtain the probability density function for the early behavior of the epidemic. This provides an appropriate distribution for the initial conditions with which to describe the subsequent deterministic evolution of the system. We apply the method of matching asymptotic expansions to link the two stages. This allows us to estimate the standard deviation of the number of infectives in the developed outbreak, and the statistical characteristics of the outbreak time. The potential trajectories caused by the stochastic nature of the contamination stage show greatest divergence at the initial and fade-out stages and coincide most tightly just after the peak of the epidemic. The time to the peak of the outbreak is not strongly dependent on the initial trajectory.     

Mutations in the heme b-binding residue of SDHC inhibit assembly of respiratory chain complex II in mammalian cells

Respiratory chain complex II has been extensively studied but little is known about its assembly and the role of its heme group. Mutations in the phylogenetically conserved histidine 127 of the SDHC subunit have been shown to abrogate heme binding in yeast and bacteria without impairing complex II assembly or enzymatic activities. Here we show that in mammalian cells these mutations lead to a complete reduction of SDHC in mitochondria, a destabilisation of SDHD and SDHB, and to an abrogation of complex II enzymatic activities, suggesting that in mammalian cells complex II assembly is more complex than in lower organisms.     

Species sorting and neutral processes are both important during the initial assembly of bacterial communities

Many studies have shown that species sorting, that is, the selection by local environmental conditions is important for the composition and assembly of bacterial communities. On the other hand, there are other studies that could show that bacterial communities are neutrally assembled. In this study, we implemented a microcosm experiment with the aim to determine, at the same time, the importance of species sorting and neutral processes for bacterial community assembly during the colonisation of new, that is, sterile, habitats, by atmospheric bacteria. For this we used outdoor microcosms, which contained sterile medium from three different rock pools representing different environmental conditions, which were seeded by rainwater bacteria. We found some evidence for neutral assembly processes, as almost every 4th taxon growing in the microcosms was also detectable in the rainwater sample irrespective of the medium. Most of these taxa belonged to widespread families with opportunistic growth strategies, such as the Pseudomonadaceae and Comamonadaceae, indicating that neutrally assembled taxa may primarily be generalists. On the other hand, we also found evidence for species sorting, as one out of three media selected a differently composed bacterial community. Species sorting effects were relatively weak and established themselves via differences in relative abundance of generalists among the different media, as well as media-specific occurrences of a few specific taxa. In summary, our results suggest that neutral and species sorting processes interact during the assembly of bacterial communities and that their importance may differ depending on how many generalists and specialists are present in a community.     

Fertilization envelope assembly in sea urchin eggs inseminated in chloride-deficient sea water: II. Biochemical effects

Eggs of the sea urchin Strongylocentrotus purpuratus were fertilized in normal and in several chloride-deficient sea waters ([ Cl-]: normal greater than isethionate greater than methyl sulfonate greater than bromide). The fertilization envelopes (FE) were thinner and failed to harden, and the characteristic I-T transition did not occur. The permeability of the experimental FEs, as determined by release of protein from the perivitelline space, increased in the order of decreasing [Cl-]. Release of the enzymes beta-1,3-glucanase and cortical granule protease were not significantly altered. On the other hand, release of ovoperoxidase was increased three to four times in bromide sea water. Furthermore, a dose-response was observed in varying concentrations of bromide-normal sea water. With decreasing chloride (increasing bromide) concentration, more ovoperoxidase activity was observed. Cytochemical localization of ovoperoxidase activity with diaminobenzidine revealed almost a total lack of staining of FEs from bromide-substituted sea water. The results suggest that in chloride-deficient sea waters protein incorporation into the nascent FE is impaired. At least in the case of bromide, the incorporation of ovoperoxidase into the nascent FE was also inhibited.     

The coalescent and the genealogical process in geographically structured population

We shall extend Kingman's coalescent to the geographically structured population model with migration among colonies. It is described by a continuous-time Markov chain, which is proved to be a dual process of the diffusion process of stepping-stone model. We shall derive a system of equations for the spatial distribution of a common ancestor of sampled genes from colonies and the mean time to getting to one common ancestor. These equations are solved in three particular models; a two-population model, the island model and the one-dimensional stepping-stone model with symmetric nearest-neighbour migration.     

Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis

The polymerase chain reaction is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. We have developed and tested efficient tools for PCR primer and probe design, which also predict oligonucleotide properties based on experimental studies of PCR efficiency. The tools provide comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, unique, group-specific, bisulphite modification assays, Overlap-Extension PCR Multi-Fragment Assembly, as well as a programme to design oligonucleotide sets for long sequence assembly by ligase chain reaction. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. It calculates the melting temperature for standard and degenerate oligonucleotides including LNA and other modifications, provides analyses for a set of primers with prediction of oligonucleotide properties, dimer and G-quadruplex detection, linguistic complexity, and provides a dilution and resuspension calculator.     

Evidence for independent mechanisms and a multiple-hit model of tau assembly

Formation of inclusions containing polymerized tau protein is a hallmark of Alzheimer's disease and related disorders. In vitro studies have demonstrated the ability of polyglycosaminoglycans and fatty acids to promote tau polymerization. In this report, we examined their impact on tau polymerization separately and together. Tau assembly with only arachidonic acid was faster than that with only heparin. The presence of dithiothreitol reduced heparin-promoted tau assembly while enhancing arachidonic acid reactions. However, simultaneous use of these molecules increased the rate of filament assembly substantially, negated the effects of the reducing agent, and has very little effect on the morphology of filaments. The increases in polymerization resulted from accelerated nucleation. Finally, a FTDP-17 mutation was identified that could complement heparin to generate assembly kinetics similar to that of wild-type tau with both inducers. Our results support a multiple-hit model where several induced changes in tau can function independently to promote tau assembly.     

Recent advances in understanding the assembly and repair of photosystem II

Background

Photosystem II (PSII) is the light-driven water:plastoquinone oxidoreductase of oxygenic photosynthesis and is found in the thylakoid membrane of chloroplasts and cyanobacteria. Considerable attention is focused on how PSII is assembled in vivo and how it is repaired following irreversible damage by visible light (so-called photoinhibition). Understanding these processes might lead to the development of plants with improved growth characteristics especially under conditions of abiotic stress.

Scope

Here we summarize recent results on the assembly and repair of PSII in cyanobacteria, which are excellent model organisms to study higher plant photosynthesis.

Conclusions

Assembly of PSII is highly co-ordinated and proceeds through a number of distinct assembly intermediates. Associated with these assembly complexes are proteins that are not found in the final functional PSII complex. Structural information and possible functions are beginning to emerge for several of these ‘assembly’ factors, notably Ycf48/Hcf136, Psb27 and Psb28. A number of other auxiliary proteins have been identified that appear to have evolved since the divergence of chloroplasts and cyanobacteria. The repair of PSII involves partial disassembly of the damaged complex, the selective replacement of the damaged sub-unit (predominantly the D1 sub-unit) by a newly synthesized copy, and reassembly. It is likely that chlorophyll released during the repair process is temporarily stored by small CAB-like proteins (SCPs). A model is proposed in which damaged D1 is removed in Synechocystis sp. PCC 6803 by a hetero-oligomeric complex composed of two different types of FtsH sub-unit (FtsH2 and FtsH3), with degradation proceeding from the N-terminus of D1 in a highly processive reaction. It is postulated that a similar mechanism of D1 degradation also operates in chloroplasts. Deg proteases are not required for D1 degradation in Synechocystis 6803 but members of this protease family might play a supplementary role in D1 degradation in chloroplasts under extreme conditions.     

A structural model for the assembly of the 30S subunit of the ribosome

The order in which proteins bind to 16S rRNA, the assembly map, was determined by Nomura and co-workers in the early 1970s. The assembly map shows the dependencies of binding of successive proteins but fails to address the relationship of these dependencies to the three-dimensional folding of the ribosome. Here, using molecular mechanics techniques, we rationalize the order of protein binding in terms of ribosomal folding. We determined the specific contacts between the ribosomal proteins and 16S rRNA from a crystal structure of the 30S subunit (1FJG). We then used these contacts as restraints in a rigid body Monte-Carlo simulation with reduced-representation models of the RNA and proteins. Proteins were added sequentially to the RNA in the order that they appear in the assembly map. Our results show that proteins nucleate the folding of the head, platform, and body domains, but they do not strongly restrict the orientations of the domains relative to one another. We also examined the contributions of individual proteins to the formation of binding sites for sequential proteins in the assembly process. Binding sites for the primary binding proteins are generally more ordered in the naked RNA than those for other proteins. Furthermore, we examined one pathway in the assembly map and found that the addition of early binding proteins helps to organize the RNA around the binding sites of proteins that bind later. It appears that the order of assembly depends on the degree of pre-organization of each protein's binding site at a given stage of assembly, and the impact that the binding of each protein has on the organization of the remaining unoccupied binding sites.